BN0952 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 7.4285e-07 7.0211e-02
Layer 4 1.6145e-04 1.1724e-03
Layer 3 2.0277e-04 8.3597e-03
Layer 5 3.3764e-04 3.1980e-03
Layer 6 7.6202e-04 9.5135e-03
WM 8.8917e-02 2.1611e-01
Layer 1 1.2331e-01 3.8261e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
COX7B Expression Distribution
Gene Specificity Score (GSS)
COX7B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
COX7B Layer 5 2.2832 0.6844
SNCA Layer 5 2.4053 0.6676
FKBP8 Layer 5 2.5059 0.6541
TLE5 Layer 5 2.3125 0.6493
ATP1A3 Layer 4 2.4297 0.6452
MDH1 Layer 4 2.3555 0.6442
RTN1 Layer 5 2.3711 0.6437
ATP5MD Layer 4 2.3242 0.6436
UQCRQ Layer 5 2.2461 0.6427
ENO2 Layer 4 2.4023 0.6424
RTN3 Layer 5 2.2832 0.6419
KIF3C Layer 4 2.1484 0.6419
COX6B1 Layer 5 2.2363 0.6415
NDUFB8 Layer 5 2.3838 0.6415
UQCR10 Layer 5 2.2393 0.6415
SYP Layer 5 2.3750 0.6404
STMN1 Layer 4 2.2969 0.6387
SPTAN1 Layer 5 2.1777 0.6374
PKM Layer 3 2.2344 0.6373
HINT1 Layer 5 2.2930 0.6355
RPS7 Layer 5 2.3496 0.6355
SELENOW Layer 5 2.2363 0.6338
AP2M1 Layer 5 2.2969 0.6338
SYT1 Layer 5 2.3926 0.6334
NDUFA3 Layer 4 2.2676 0.6333
APLP2 Layer 4 2.1348 0.6327
SLC25A3 Layer 4 2.0723 0.6323
WBP2 Layer 5 2.1348 0.6320
TUBB2A Layer 5 2.5723 0.6312
COX7A2 Layer 4 2.2578 0.6293
APP Layer 4 2.2461 0.6286
SNRPN Layer 4 2.2324 0.6284
FAIM2 Layer 4 2.3750 0.6282
C12orf57 Layer 4 2.2578 0.6268
ATP5MPL Layer 5 2.2422 0.6268
PPIA Layer 5 2.1152 0.6264
EVL Layer 4 2.2227 0.6263
NDUFB1 Layer 5 2.1621 0.6262
ATP1A1 Layer 4 2.2520 0.6258
RTL8C Layer 4 2.0820 0.6256
CALY Layer 4 2.5332 0.6253
DNM1 Layer 4 2.3125 0.6253
ATP6V0C Layer 4 2.4082 0.6251
CPLX1 Layer 4 2.4844 0.6251
ATP6V1F Layer 4 2.1445 0.6251
GOT1 Layer 5 2.2930 0.6248
UQCRH Layer 4 2.3965 0.6247
NACA Layer 5 2.1719 0.6244
PFN2 Layer 4 2.3027 0.6237
YWHAG Layer 5 2.4121 0.6231

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0952
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0952_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0952/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0952/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0952/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0952/report/PD/BN0952_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0952/report/PD/BN0952_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:58:52
  • Number of Processes: 10
  • Spending Time: 0h 3m